I had very rusty leeks last year, and very very rusty garlic! I pulled off some of the leaves, but it seemed daft to me because all I did was expose nice clean layers, which within a week or so, we rusty! The leeks didn't suffer and were edible and yummy. The garlic was okay, but one lot, and I can't remember which lot, might have been Solent White, were badly affected and I dug them early and they weren't as big as they could have been. But, they were perfectly useable.
Don't know how to treat it, other than make sure you rotate well, but I have my leeks right up the other end of my plot this year, and already they are showing signs of rust! >:(